NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	314.09
Volume:	288.394
LogP:	3.896
LogD:	3.767
LogS:	-3.891
# Rotatable Bonds:	9
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.614
Synthetic Accessibility Score:	3.993
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.598
MDCK Permeability:	2.0373508959892206e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.192
Plasma Protein Binding (PPB):	97.53015899658203%
Volume Distribution (VD):	0.345
Pgp-substrate:	2.6488451957702637%

ADMET: Metabolism

CYP1A2-inhibitor:	0.143
CYP1A2-substrate:	0.729
CYP2C19-inhibitor:	0.097
CYP2C19-substrate:	0.701
CYP2C9-inhibitor:	0.185
CYP2C9-substrate:	0.985
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.829
CYP3A4-inhibitor:	0.089
CYP3A4-substrate:	0.158

ADMET: Excretion

Clearance (CL):	1.64
Half-life (T1/2):	0.846

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.928
Drug-inuced Liver Injury (DILI):	0.904
AMES Toxicity:	0.555
Rat Oral Acute Toxicity:	0.92
Maximum Recommended Daily Dose:	0.883
Skin Sensitization:	0.925
Carcinogencity:	0.828
Eye Corrosion:	0.38
Eye Irritation:	0.632
Respiratory Toxicity:	0.957

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC53302

Natural Product ID:	NPC53302
*Common Name:**	Majusculoic Acid
IUPAC Name:	3-[(1S,2S)-2-[(3E,5Z)-6-bromonona-3,5-dienyl]cyclopropyl]propanoic acid
Synonyms:	Majusculoic Acid
Standard InCHIKey:	XSRLEFWNCQOETJ-SULJWLEGSA-N
Standard InCHI:	InChI=1S/C15H23BrO2/c1-2-6-14(16)8-5-3-4-7-12-11-13(12)9-10-15(17)18/h3,5,8,12-13H,2,4,6-7,9-11H2,1H3,(H,17,18)/b5-3+,14-8-/t12-,13-/m0/s1
SMILES:	CCC/C(=C/C=C/CC[C@H]1C[C@@H]1CCC(=O)O)/Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL465603
PubChem CID:	11602110
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0000495] Carbocyclic fatty acids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO32831	cyanobacterial mat assemblage	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[15844960]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
MIC	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	8000.0	nM	PMID[568922]
NPT554	Organism	Candida glabrata	Candida glabrata	MIC	=	19300.0	nM	PMID[568922]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC53302 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	212
0.1-0.2	1614
0.2-0.3	11854
0.3-0.4	17329
0.4-0.5	8502
0.5-0.6	2874
0.6-0.7	276
0.7-0.8	35
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7692	Intermediate Similarity	NPC18951
0.7681	Intermediate Similarity	NPC234767
0.7647	Intermediate Similarity	NPC125312
0.7647	Intermediate Similarity	NPC174560
0.7619	Intermediate Similarity	NPC281245
0.7576	Intermediate Similarity	NPC225929
0.75	Intermediate Similarity	NPC139029
0.75	Intermediate Similarity	NPC294548
0.75	Intermediate Similarity	NPC36061
0.75	Intermediate Similarity	NPC1813
0.7467	Intermediate Similarity	NPC3753
0.7467	Intermediate Similarity	NPC237591
0.7432	Intermediate Similarity	NPC288667
0.7385	Intermediate Similarity	NPC88966
0.7385	Intermediate Similarity	NPC290563
0.7385	Intermediate Similarity	NPC25417
0.7385	Intermediate Similarity	NPC87564
0.7385	Intermediate Similarity	NPC6095
0.7385	Intermediate Similarity	NPC85813
0.7385	Intermediate Similarity	NPC281972
0.7385	Intermediate Similarity	NPC261831
0.7385	Intermediate Similarity	NPC32467
0.7385	Intermediate Similarity	NPC154245
0.7385	Intermediate Similarity	NPC424
0.7368	Intermediate Similarity	NPC476844
0.7361	Intermediate Similarity	NPC60120
0.726	Intermediate Similarity	NPC476614
0.7246	Intermediate Similarity	NPC251042
0.7246	Intermediate Similarity	NPC174447
0.7246	Intermediate Similarity	NPC122521
0.7237	Intermediate Similarity	NPC301065
0.7231	Intermediate Similarity	NPC321062
0.7231	Intermediate Similarity	NPC70387
0.7222	Intermediate Similarity	NPC308294
0.7222	Intermediate Similarity	NPC142423
0.7206	Intermediate Similarity	NPC329819
0.7206	Intermediate Similarity	NPC267817
0.7188	Intermediate Similarity	NPC48162
0.7164	Intermediate Similarity	NPC477201
0.7164	Intermediate Similarity	NPC187777
0.7164	Intermediate Similarity	NPC179764
0.7143	Intermediate Similarity	NPC40082
0.7123	Intermediate Similarity	NPC278895
0.7089	Intermediate Similarity	NPC169095
0.7077	Intermediate Similarity	NPC92114
0.7051	Intermediate Similarity	NPC309399
0.7031	Intermediate Similarity	NPC224227
0.7015	Intermediate Similarity	NPC274290
0.7015	Intermediate Similarity	NPC67367
0.7015	Intermediate Similarity	NPC228473
0.7015	Intermediate Similarity	NPC473863
0.7015	Intermediate Similarity	NPC54766
0.7013	Intermediate Similarity	NPC213223
0.7013	Intermediate Similarity	NPC183503
0.7013	Intermediate Similarity	NPC55527
0.7013	Intermediate Similarity	NPC103958
0.7013	Intermediate Similarity	NPC161923
0.7013	Intermediate Similarity	NPC283908
0.6986	Remote Similarity	NPC166791
0.6986	Remote Similarity	NPC322035
0.6986	Remote Similarity	NPC100719
0.6984	Remote Similarity	NPC180534
0.6962	Remote Similarity	NPC120776
0.6962	Remote Similarity	NPC240170
0.6923	Remote Similarity	NPC472327
0.6923	Remote Similarity	NPC279666
0.6923	Remote Similarity	NPC262968
0.6923	Remote Similarity	NPC192540
0.6892	Remote Similarity	NPC472875
0.6883	Remote Similarity	NPC35656
0.6875	Remote Similarity	NPC149821
0.6875	Remote Similarity	NPC5413
0.6866	Remote Similarity	NPC87394
0.6857	Remote Similarity	NPC274927
0.6857	Remote Similarity	NPC106851
0.6849	Remote Similarity	NPC245947
0.6849	Remote Similarity	NPC318420
0.6849	Remote Similarity	NPC326268
0.6849	Remote Similarity	NPC136164
0.6849	Remote Similarity	NPC255863
0.6842	Remote Similarity	NPC475310
0.6835	Remote Similarity	NPC69143
0.6835	Remote Similarity	NPC469514
0.6818	Remote Similarity	NPC216407
0.6806	Remote Similarity	NPC322457
0.6795	Remote Similarity	NPC476046
0.6795	Remote Similarity	NPC251970
0.6795	Remote Similarity	NPC472966
0.6795	Remote Similarity	NPC241854
0.679	Remote Similarity	NPC274996
0.679	Remote Similarity	NPC158846
0.679	Remote Similarity	NPC196827
0.6769	Remote Similarity	NPC59051
0.6765	Remote Similarity	NPC45626
0.6765	Remote Similarity	NPC477984
0.6761	Remote Similarity	NPC243532
0.6761	Remote Similarity	NPC235242
0.6757	Remote Similarity	NPC197089
0.6757	Remote Similarity	NPC304665
0.6757	Remote Similarity	NPC126899
0.6757	Remote Similarity	NPC154728
0.6753	Remote Similarity	NPC160817
0.6719	Remote Similarity	NPC207292
0.6716	Remote Similarity	NPC39633
0.6716	Remote Similarity	NPC139545
0.6716	Remote Similarity	NPC309606
0.6714	Remote Similarity	NPC34416
0.6712	Remote Similarity	NPC68343
0.6712	Remote Similarity	NPC328089
0.6711	Remote Similarity	NPC67608
0.6709	Remote Similarity	NPC201027
0.6709	Remote Similarity	NPC476795
0.6667	Remote Similarity	NPC179028
0.6667	Remote Similarity	NPC312480
0.6667	Remote Similarity	NPC28205
0.6667	Remote Similarity	NPC201939
0.6667	Remote Similarity	NPC325977
0.6667	Remote Similarity	NPC476626
0.6627	Remote Similarity	NPC142244
0.6625	Remote Similarity	NPC279537
0.6623	Remote Similarity	NPC67183
0.6585	Remote Similarity	NPC113363
0.6582	Remote Similarity	NPC306928
0.6582	Remote Similarity	NPC476649
0.6567	Remote Similarity	NPC129458
0.6567	Remote Similarity	NPC18357
0.6548	Remote Similarity	NPC296367
0.6543	Remote Similarity	NPC281296
0.6543	Remote Similarity	NPC97377
0.6543	Remote Similarity	NPC476608
0.6543	Remote Similarity	NPC316324
0.6543	Remote Similarity	NPC165711
0.6543	Remote Similarity	NPC471897
0.6543	Remote Similarity	NPC107039
0.6543	Remote Similarity	NPC471899
0.6543	Remote Similarity	NPC61952
0.6538	Remote Similarity	NPC29328
0.6538	Remote Similarity	NPC320119
0.6522	Remote Similarity	NPC52264
0.6522	Remote Similarity	NPC28779
0.6522	Remote Similarity	NPC10316
0.6522	Remote Similarity	NPC128061
0.6522	Remote Similarity	NPC200845
0.6522	Remote Similarity	NPC223677
0.65	Remote Similarity	NPC255060
0.6494	Remote Similarity	NPC199557
0.6494	Remote Similarity	NPC143396
0.6494	Remote Similarity	NPC469914
0.6486	Remote Similarity	NPC53642
0.6486	Remote Similarity	NPC470325
0.6486	Remote Similarity	NPC470320
0.6471	Remote Similarity	NPC225066
0.6471	Remote Similarity	NPC10081
0.6471	Remote Similarity	NPC71761
0.6471	Remote Similarity	NPC310470
0.6471	Remote Similarity	NPC70834
0.6471	Remote Similarity	NPC83569
0.6471	Remote Similarity	NPC102197
0.6471	Remote Similarity	NPC69279
0.6463	Remote Similarity	NPC260385
0.6463	Remote Similarity	NPC59436
0.6463	Remote Similarity	NPC198240
0.6463	Remote Similarity	NPC321514
0.6463	Remote Similarity	NPC218817
0.6463	Remote Similarity	NPC11796
0.6463	Remote Similarity	NPC239098
0.6463	Remote Similarity	NPC110094
0.6463	Remote Similarity	NPC280654
0.6463	Remote Similarity	NPC121200
0.6463	Remote Similarity	NPC192006
0.6463	Remote Similarity	NPC74410
0.6462	Remote Similarity	NPC216130
0.6462	Remote Similarity	NPC91495
0.6456	Remote Similarity	NPC470237
0.6456	Remote Similarity	NPC321017
0.6456	Remote Similarity	NPC326024
0.6438	Remote Similarity	NPC328776
0.6438	Remote Similarity	NPC320305
0.6437	Remote Similarity	NPC6247
0.6437	Remote Similarity	NPC116575
0.642	Remote Similarity	NPC110461
0.642	Remote Similarity	NPC180886
0.642	Remote Similarity	NPC12740
0.642	Remote Similarity	NPC472967
0.642	Remote Similarity	NPC899
0.642	Remote Similarity	NPC239127
0.642	Remote Similarity	NPC266159
0.642	Remote Similarity	NPC89294
0.642	Remote Similarity	NPC61863
0.6418	Remote Similarity	NPC470412
0.6418	Remote Similarity	NPC284212
0.6418	Remote Similarity	NPC470410
0.641	Remote Similarity	NPC476660
0.641	Remote Similarity	NPC318766
0.6406	Remote Similarity	NPC314679
0.6406	Remote Similarity	NPC117572
0.64	Remote Similarity	NPC474329
0.64	Remote Similarity	NPC474304
0.6395	Remote Similarity	NPC476038
0.6395	Remote Similarity	NPC194937

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC53302 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	178
0.1-0.2	2316
0.2-0.3	4198
0.3-0.4	1741
0.4-0.5	567
0.5-0.6	130
0.6-0.7	16
0.7-0.8	4
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.75	Intermediate Similarity	NPD3172	Approved
0.7385	Intermediate Similarity	NPD4266	Approved
0.7385	Intermediate Similarity	NPD3196	Approved
0.7385	Intermediate Similarity	NPD3194	Approved
0.7385	Intermediate Similarity	NPD3195	Phase 2
0.6984	Remote Similarity	NPD622	Approved
0.6923	Remote Similarity	NPD28	Approved
0.6923	Remote Similarity	NPD29	Approved
0.6875	Remote Similarity	NPD3173	Approved
0.6486	Remote Similarity	NPD3197	Phase 1
0.6406	Remote Similarity	NPD634	Phase 3
0.6406	Remote Similarity	NPD3174	Discontinued
0.6406	Remote Similarity	NPD4222	Approved
0.6324	Remote Similarity	NPD3186	Phase 1
0.6316	Remote Similarity	NPD7331	Phase 2
0.631	Remote Similarity	NPD5368	Approved
0.6301	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.6296	Remote Similarity	NPD8039	Approved
0.6265	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6235	Remote Similarity	NPD857	Phase 3
0.6235	Remote Similarity	NPD5369	Approved
0.6235	Remote Similarity	NPD226	Approved
0.6222	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6222	Remote Similarity	NPD6101	Approved
0.6184	Remote Similarity	NPD7341	Phase 2
0.6163	Remote Similarity	NPD4270	Approved
0.6163	Remote Similarity	NPD6435	Approved
0.6163	Remote Similarity	NPD4269	Approved
0.6154	Remote Similarity	NPD39	Approved
0.6118	Remote Similarity	NPD4252	Approved
0.6092	Remote Similarity	NPD7154	Phase 3
0.6092	Remote Similarity	NPD5362	Discontinued
0.6087	Remote Similarity	NPD5281	Approved
0.6087	Remote Similarity	NPD5284	Approved
0.6087	Remote Similarity	NPD6411	Approved
0.6071	Remote Similarity	NPD4271	Approved
0.6071	Remote Similarity	NPD3732	Approved
0.6071	Remote Similarity	NPD4268	Approved
0.6044	Remote Similarity	NPD5346	Phase 2
0.6044	Remote Similarity	NPD800	Approved
0.6044	Remote Similarity	NPD5347	Phase 2
0.6022	Remote Similarity	NPD5779	Approved
0.6022	Remote Similarity	NPD5778	Approved
0.5978	Remote Similarity	NPD1086	Approved
0.5978	Remote Similarity	NPD1090	Approved
0.5978	Remote Similarity	NPD1089	Approved
0.5955	Remote Similarity	NPD5363	Approved
0.5952	Remote Similarity	NPD4756	Discovery
0.593	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.593	Remote Similarity	NPD4819	Approved
0.593	Remote Similarity	NPD4820	Approved
0.593	Remote Similarity	NPD4822	Approved
0.593	Remote Similarity	NPD4821	Approved
0.5915	Remote Similarity	NPD615	Clinical (unspecified phase)
0.5914	Remote Similarity	NPD7983	Approved
0.5909	Remote Similarity	NPD9491	Approved
0.5889	Remote Similarity	NPD5786	Approved
0.5882	Remote Similarity	NPD225	Approved
0.5882	Remote Similarity	NPD227	Approved
0.587	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.5851	Remote Similarity	NPD1088	Approved
0.5846	Remote Similarity	NPD5326	Phase 3
0.5824	Remote Similarity	NPD4793	Discontinued
0.5823	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5795	Remote Similarity	NPD5209	Approved
0.5789	Remote Similarity	NPD4193	Approved
0.5789	Remote Similarity	NPD4191	Approved
0.5789	Remote Similarity	NPD4194	Approved
0.5789	Remote Similarity	NPD5122	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD4192	Approved
0.5761	Remote Similarity	NPD4518	Approved
0.5747	Remote Similarity	NPD4695	Discontinued
0.573	Remote Similarity	NPD5331	Approved
0.573	Remote Similarity	NPD5332	Approved
0.5729	Remote Similarity	NPD1693	Approved
0.5714	Remote Similarity	NPD9448	Phase 2
0.5714	Remote Similarity	NPD77	Approved
0.5714	Remote Similarity	NPD633	Phase 3
0.5714	Remote Similarity	NPD4694	Approved
0.5714	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD9450	Approved
0.5714	Remote Similarity	NPD5279	Phase 3
0.5714	Remote Similarity	NPD5280	Approved
0.5682	Remote Similarity	NPD4790	Discontinued
0.567	Remote Similarity	NPD7839	Suspended
0.5652	Remote Similarity	NPD1087	Approved
0.5638	Remote Similarity	NPD5785	Approved
0.5638	Remote Similarity	NPD6698	Approved
0.5638	Remote Similarity	NPD7838	Discovery
0.5638	Remote Similarity	NPD46	Approved
0.5638	Remote Similarity	NPD5207	Approved
0.5618	Remote Similarity	NPD4223	Phase 3
0.5618	Remote Similarity	NPD3667	Approved
0.5618	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD4221	Approved
0.5616	Remote Similarity	NPD342	Phase 1

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data